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bridgman: Those aticonfig commands are for the fglrx binary drivers. They will not do anything with the radeonhd driver. You can do something similar with xrandr 1.2 when running radeonhd.

Yeah, that's what puzzled me. Your post listed the aticonfig commands and said they had fixed the black border problem, but also said that you had switched to the radeonhd driver. The only other interpretation I could think of was that the commands fixed your problem with fglrx but you switched to radeonhd anyways.

unsuable to the point where I think pluging back my 6600GT in the other pci express socket as a backup

the problem is that my native resolution for the screen is 1920x1080 and that the computer still display 1920x1080 but they are not 1 per 1 pixel and downscaled to fit inside the black borders.
I can't take a picture sorry.

So for exemple the empty Xorg display that you get by just running X, doesn't display what it should, and you can imagine how look policies with this

We asked some questions internally, it looks like a default setting for HDMI was changed in the common code. This has triggered a number of monitors to underscan.

Note that this does not happen on all HDTV monitors, some actually need this setting to have a normal near-pixel perfect screen.

To override this setting try setting this value and restarting X.

aticonfig --set-pcs-val=MCIL,DigitalHDTVDefaultUnderscan,0

To enable this functionality through the configuration tools it will not come for a number of releases, since this setting is quite deep under the covers and there are other issues that will need to be resolved to fix this fully.